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gyorilab / adeft

Tool for disambiguating acronyms and abbreviations in text for NLP applications
BSD 2-Clause "Simplified" License
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Some non-standard names in models #69

Closed bgyori closed 3 years ago

bgyori commented 3 years ago

Some models contain names for groundings that aren't standard in some way. The list below list these cases in the order: shortform, namespace, ID, current name in the model, standard name (per the INDRA ontology):

CAS UP P38605 Cycloartenol synthase CAS1
DOG1 UP A0SVK0 Protein DELAY OF GERMINATION 1 DOG1
MT CHEBI CHEBI:2089 O-methylserotonin 5-methoxytryptamine
SAK UP P68802 Staphylokinase sak
SD MESH D012929 Social Distance Psychological Distance
SDs MESH D012929 Social Distance Psychological Distance
SIN HGNC 16898 SIN EFS
EC MESH D004759 Cell, Enterochromaffin Enterochromaffin Cells
MOS CHEBI CHEBI:31867 Mosapride citrate mosapride citrate dihydrate
PKL UP Q9S775 CHD3-type chromatin-remodeling factor PICKLE PKL
SN MESH D008836 Staphylococcal nuclease Micrococcal Nuclease
MB MESH C033575 N-acetylmuramyl-alanylglutamine-n-butyl ester murabutide
PRK UP P25697 Phosphoribulokinase, chloroplastic At1g32060
AR GO GO:0007340 Acrosome Reaction acrosome reaction
FER UP Q9SCZ4 Receptor-like protein kinase FERONIA FER
NP FPLX Natriuretic_peptide Natriuretic Peptide Natriuretic_peptide
NPs FPLX Natriuretic_peptide Natriuretic Peptide Natriuretic_peptide
RSE MESH D000076962 High-Intensity Interval Training Receptors, Chimeric Antigen
TF CHEBI CHEBI:136609 Theaflavin theaflavin
TF CHEBI CHEBI:75182 Toylfluanid tolylfluanid
TR CHEBI CHEBI:51247 Texas red texas red
TG CHEBI CHEBI:9516 Thapsigargin thapsigargin

I think the only questionable cases here are for UP where Adeft lists protein names whereas in INDRA the corresponding gene name is considered the standard. The other cases are straightforward and should probably be replaced.

steppi commented 3 years ago

I'll change all of them to be in line with INDRA's standard. For the RSE example it looks like the grounding and name do not even match. I'll inspect that one to see what the correct name and grounding should be.

steppi commented 3 years ago

Done. Besides the RSE example, there was also an incorrect grounding of social distance to the MeSH term for psychological distance. I found an NCIT grounding for social distance to use instead.

bgyori commented 3 years ago

Great, thanks for looking into this!